The mvTool universal variant converter can convert the various combinations of these formats into a standard variant list in the rCRS-based HGVS (1-3) formats.

The current mtDNA variant data is mostly based on the default revised Cambridge sequence (rCRS, accession number NC_012920.1). The use of YRI (Yoruban, accession number NC_001807.4, derived from AF347015) as the mitochondrial reference genome is discouraged by NCBI. Since some commercial SNP array platforms used or may still use YRI as the reference genome, mvTool can convert YRI-based positions into rCRS-based positions, but only for backward compatibility. The mvTool does not covert rCRS coordinates to YRI-based coordinates.

Running mvTool:

mvTool functions in two modes, “Web” and “API.” In Web mode, the user can paste a list of mtDNA variants into the Web form and have annotations returned as either an HTML table or as a downloadable Excel file. The input form is prepopulated with example variants in mixed formats to enable quick start, and includes help documentation describing the technical details shown when the tool is first opened. Upon submission, each job is sent to a 24‐CPU dedicated server with 32 GB of RAM and 4 TB of HDD. With this set‐up, most analyses of one mtDNA genome (usually comprised of less than 100 variants) take under 1 min to complete.

In the API mode, users can use the UNIX curl command to remotely upload a file in VCF, HGVS, or classical mtDNA variant formats to retrieve annotation back as either JSON or annotated VCF files. There are three ways to access MSeqDR mvTool API, using syntax similar to the following example commands:

mvTool is updated with data from Mitomap 2018 Update #3 (September 1, 2018) which added 125 new variants from 598 new full-length (FL) and 445 control region (CR) GenBank sequences. This brings the Mitomap total of non-disease variants to 13,656, the number of FL sequences to 46,092.

Input mtDNA variants in any of the 7 major formats, mixed formats input is supported. The results are returned as multiple html tables, as well as a downloadable combined Excel file. An API is implemented, which takes inputs in VCF, HGVS, or classical mtDNA variant nomenclatures, and returns annotated vcf or json outputs.